After dislodging the reed from Squidward's throat, Patrick accidentally turns the submarine back to large size, causing SpongeBob and him to be stuck in the submarine, which is still inside Squidward.
"Hide and Then What Happens?"
SpongeBob uses it to find Patrick.
Sandy uses it to go to the surface to retrieve air. However, SpongeBob opens the hatch underwater, letting all the water in it, during which Sandy nearly suffocated.
"It Came from Goo Lagoon"
Sandy, as well as Patrick and SpongeBob, follow the goo bubble and find out what's causing it to move.
In the game, SpongeBob and Patrick control Sandy's submarine and go down Squidward's throat. The player moves the submarine by moving the cursor. Clicking on the mouse button shoots a projectile. Shooting at bubbles scores points. Collecting clarinet reeds gives the following upgrades in order: rapid fire (the mouse button can be held for continuous fire), score x2, score x4, double shot (every shot can penetrate through two bubbles), then the rest gives 500 points. Bumping into a bubble or the edges will remove all upgrades, reverting the submarine back to its original state. Bumping into too many bubbles or the edges will result in a game over.
It's revealed in "It Came from Goo Lagoon" that Sandy has missiles in her submarine in case she gets stuck in traffic.